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Resource: The full-length transcriptome of C. elegans using direct RNA sequencing
- Nathan P. Roach,
- Norah Sadowski,
- Amelia F. Alessi,
- Winston Timp,
- James Taylor,
- and John K. Kim
Genome Res. February 2020 30: 299-312; Published in Advance February 5, 2020, doi:10.1101/gr.251314.119
...: In this window In a new window Figure 1. Overview of approach and sequencing of full-length isoforms. (A) Diagram of the C. elegans life cycle. (B) Plot of normalized coverage across the average coding gene with full-length (green), non-full-length (blue), and all reads (red) considered. (C) Percentage of reads...
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Resource: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
- Runsheng Li,
- Xiaoliang Ren,
- Qiutao Ding,
- Yu Bi,
- Dongying Xie,
- and Zhongying Zhao
Genome Res. February 2020 30: 287-298; Published in Advance February 5, 2020, doi:10.1101/gr.251512.119
...developmental stages determined by the long reads in this study and by the existing RNA-seq reads (WormBase release WS260). (B) An example of stage-specific abundance of TrackCluster predicted isoforms. Shaded in light blue is the coverage of long reads for gene efhd-1 over development. Existing (black...
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Resource: Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome
- Kourosh Salehi-Ashtiani,
- Chenwei Lin,
- Tong Hao,
- Yun Shen,
- David Szeto,
- Xinping Yang,
- Lila Ghamsari,
- HanJoo Lee,
- Changyu Fan,
- Ryan R. Murray,
- Stuart Milstein,
- Nenad Svrzikapa,
- Michael E. Cusick,
- Frederick P. Roth,
- David E. Hill,
- and Marc Vidal
Genome Res. December 2009 19: 2334-2342; Published in Advance October 2, 2009, doi:10.1101/gr.098640.109
...available for 10 years, the exact transcript structures of many of its protein-coding genes remain unsettled. Approximately two-thirds of the ORFeome has been verified reactively by amplifying and cloning computationally predicted transcript models; still a full third of the ORFeome remains experimentally...
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RESOURCE: Toward Improving Caenorhabditis elegans Phenome Mapping With an ORFeome-Based RNAi Library
- Jean-François Rual,
- Julian Ceron,
- John Koreth,
- Tong Hao,
- Anne-Sophie Nicot,
- Tomoko Hirozane-Kishikawa,
- Jean Vandenhaute,
- Stuart H. Orkin,
- David E. Hill,
- Sander van den Heuvel,
- and Marc Vidal
Genome Res. October 15, 2004 14: 2162-2168; doi:10.1101/gr.2505604
.... ↵ Lamesch, P., Milstein, S., Hao, T., Rosenberg, J., Li, N., Sequerra, R., Bosak, S., Doucette-Stamm, L., Vandenhaute, J., Hill, D.E., et al. 2004 . C. elegans ORFeome Version 3.1: Increasing the coverage of ORFeome resources with improved gene predictions. Genome Res . (this issue). ↵ Lee, S.S., Lee, R...
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RESOURCE: Human ORFeome Version 1.1: A Platform for Reverse Proteomics
- Jean-François Rual,
- Tomoko Hirozane-Kishikawa,
- Tong Hao,
- Nicolas Bertin,
- Siming Li,
- Amélie Dricot,
- Ning Li,
- Jennifer Rosenberg,
- Philippe Lamesch,
- Pierre-Olivier Vidalain,
- Tracey R. Clingingsmith,
- James L. Hartley,
- Dominic Esposito,
- David Cheo,
- Troy Moore,
- Blake Simmons,
- Reynaldo Sequerra,
- Stephanie Bosak,
- Lynn Doucette-Stamm,
- Christian Le Peuch,
- Jean Vandenhaute,
- Michael E. Cusick,
- Joanna S. Albala,
- David E. Hill,
- and Marc Vidal
Genome Res. October 15, 2004 14: 2128-2135; doi:10.1101/gr.2973604
..., S., Hao, T., Rosenberg, J., Li, N., Sequerra, R., Bosak, S., Doucette-Stamm, L., Vandenhaute, J., Hill, D., et al. 2004 . C. elegans ORFeome version 3.1: Increasing the coverage of ORFeome resources with improved gene predictions. Genome Res. (this issue). ↵ Lander, E.S., Linton, L.M., Birren, B...
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RESOURCE: Generation of the Brucella melitensis ORFeome Version 1.1
- Amélie Dricot,
- Jean-François Rual,
- Philippe Lamesch,
- Nicolas Bertin,
- Denis Dupuy,
- Tong Hao,
- Christophe Lambert,
- Régis Hallez,
- Jean-Marc Delroisse,
- Jean Vandenhaute,
- Ignacio Lopez-Goñi,
- Ignacio Moriyon,
- Juan M. Garcia-Lobo,
- Félix J. Sangari,
- Alastair P. MacMillan,
- Sally J. Cutler,
- Adrian M. Whatmore,
- Stephanie Bozak,
- Reynaldo Sequerra,
- Lynn Doucette-Stamm,
- Marc Vidal,
- David E. Hill,
- Jean-Jacques Letesson,
- and Xavier De Bolle
Genome Res. October 15, 2004 14: 2201-2206; doi:10.1101/gr.2456204
..., R., Bosak, S., Doucette-Stamm, L., Vandenhaute, J., Hill, D.E., et al. 2004 . C. elegans ORFeome Version 3.1: Increasing the coverage of ORFeome resources with improved gene predictions. Genome Res . (this issue). ↵ Lesser, C.F. and Miller, S.I. 2001 . Expression of microbial virulence proteins...
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LETTER: New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones
- Anita G. Fernandez,
- Kristin C. Gunsalus,
- Jerry Huang,
- Ling-Shiang Chuang,
- Nancy Ying,
- Hsiao-lan Liang,
- Caroline Tang,
- Aaron J. Schetter,
- Charles Zegar,
- Jean-François Rual,
- David E. Hill,
- Valerie Reinke,
- Marc Vidal,
- and Fabio Piano
Genome Res. February 2005 15: 250-259; doi:10.1101/gr.3194805
...New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones Anita G. Fernandez 1 , 4 , Kristin C. Gunsalus 1 , 4 , Jerry Huang 1 , Ling-Shiang Chuang 1 , Nancy Ying 1 , Hsiao-lan Liang 1...
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Methods: Shifted Transversal Design smart-pooling for high coverage interactome mapping
- Xiaofeng Xin,
- Jean-François Rual,
- Tomoko Hirozane-Kishikawa,
- David E. Hill,
- Marc Vidal,
- Charles Boone,
- and Nicolas Thierry-Mieg
Genome Res. July 2009 19: 1262-1269; Published in Advance May 15, 2009, doi:10.1101/gr.090019.108
.... BMC Bioinformatics 9: 256. doi: 10.1186/1471-2105-9-256. Lamesch P, Milstein S, Hao T, Rosenberg J, Li N, Sequerra R, Bosak S, Doucette-Stamm L, Vandenhaute J, Hill DE, et al. 2004. C. elegans ORFeome version 3.1: Increasing the coverage of ORFeome resources with improved gene predictions. Genome Res...
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PERSPECTIVE: ORFeome Cloning and Systems Biology: Standardized Mass Production of the Parts From the Parts-List
- Michael A. Brasch,
- James L. Hartley,
- and Marc Vidal
Genome Res. October 15, 2004 14: 2001-2009; doi:10.1101/gr.2769804
...from ORF minipools ( Reboul et al. 2003 ). Incorporating four years of improved gene annotations, the WS100-derived version of the C. elegans predicted ORFeome provides corrections for ∼3000 ORFs that were not obtained in Version 1.1. By redesigning new PCR primers for these repredicted ORFs, we were...
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Methods: Efficient target-selected mutagenesis in Caenorhabditis elegans: Toward a knockout for every gene
- Edwin Cuppen,
- Eelke Gort,
- Esther Hazendonk,
- Josine Mudde,
- José van de Belt,
- Isaäc J. Nijman,
- Victor Guryev,
- and Ronald H.A. Plasterk
Genome Res. May 2007 17: 649-658; Published in Advance April 6, 2007, doi:10.1101/gr.6080607
...collection of EMS-induced point mutations after mutagenesis of an animal. Extrapolation of our results indicates that knockouts for &gt;90% of all C. elegans genes are present in the current resource. We calculated that the screening complexity for -wide identification of knockouts can be decreased by two...

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